Admin - Cell Biology 16 The Cell A Molecular Approach Cooper 153 CH 2 The Compositions of Cells 7877

CELL BIOLOGY - COOPER 4E
CH. 2-THE COMPOSITIONS OF CELLS
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CONCEPT: SMALL MOLECULES
● The properties of water are crucial for cell activity

□ Water is a universal solvent, which means it can _______________________ many types of molecules
- Water makes up >70% of the cell’s weight
- In water hydrophilic molecules dissolve, hydrophobic molecules do not dissolve
□ Water (H2O) is polar, which is an uneven distribution of _____________________ within the water molecule
- Oxygen draws electrons towards it giving it a slight negative charge and hydrogens a slight positive
□ Water molecules are cohesive because the polar nature allows for water molecules to stick together
- Cohesion allows water to act as a temperature stabilizing molecule
- has high specific heat = amount of absorbed heat per gram to raise temperature by 1oC
EXAMPLE: Water molecule demonstrating polarity
● The properties of carbon are also crucial for cell activity

□ The carbon atom can bind up to four molecules at once
- Most likely to bond with Oxygen, Hydrogen, Nitrogen, and Sulfur
□ Carbon bonds through covalent bonds and these are extremely ____________________________
- Bond energy measures the amount of energy needed to break a bond (calories/mole)
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□ Carbon molecules can have multiple configurations as carbon can bind to __________________ molecules
- Stereoisomers are carbon molecules with the same chemical nature but are mirrored structures
- Two stereoisomer conformations are possible for an asymmetric carbon atom (chiral center)
□ Functional groups found on large carbon molecules confer particular characteristics onto the molecule
EXAMPLE: Carbon stereoisomers
PRACTICE
1. Which of the following is not a property of water?

a. It is a universal solvent
b. It is polar
c. It dissolves hydrophobic molecules
d. It has a high specific heat
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2. Which type of molecule dissolves in water?

a. Hydrophobic
b. Hydrophilic
c. Amphipathic
3. A carbon atom can bind how many independent molecules at once?

a. 1
b. 2
c. 3
d. 4
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CONCEPT: FOUR CLASSES OF MACROMOLECULES
● Polysaccharides are sugars (carbohydrates) that are responsible for cellular energy storage and support
□ Monosaccharides are the building blocks that make up ________________________ polysaccharides
- Covalent glycosidic bonds between a carbon and hydroxyl (OH) attach two monosaccharides together
- Can form into linear or ring structures – (CH2O)n
□ Aldose and Ketose are the two _______________________ of polysaccharides
- The class is determined based on the position of the carbonyl group (C=O)
EXAMPLE: Ketose (C=O in middle) vs. Aldose structure (C=O on end)
□ Starch, Cellulose, and Glycogen are the three main storage and structural polysaccharides in cells
- In plant cells, energy is stored as starch and structural support is provided by cellulose
- In animal cells, glycogen stores surplus chemical energy
□ Sugars are named by the ______________________________ of subunits they contain
- Mono- = 1 subunit; Di- = 2 subunits; Oligo- = up to 10 subunits, Poly- = 11+ subunits
- Common sugars include: Glucose (mono); Sucrose (Di); Lactose (Di); Amylose (Poly)
□ Glycolipids are sugars attached to lipids; Glycoproteins are sugars attached to proteins
EXAMPLE: Amylose is a linear polysaccharide made up of α(1→4) bonds
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● Nucleic acids are the subunits of DNA and RNA which are responsible for storing and transmitting genetic information
□ Each nucleotide contains a base, a five carbon sugar (deoxyribose or ribose), and a phosphate group
- There are two classes of bases: Purines with a pair of fused rings and Pyrimidines with a single ring
- Adenine (A) and Guanine (G) = purines; Cytosine (C), Thymine (T), and Uracil (U) = pyrimidines
□ Phosphodiester bonds are responsible for ____________________________ nucleic acids together
- Linear sequence of nucleic acids is important because it encodes genetic information
□ Nucleotides can also store energy
- Adenosine tri-phosphate (ATP) is a nucleotide that supplies energy for numerous cellular reactions
EXAMPLE: Complementary nucleotides bound in a DNA molecule
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● Proteins are macromolecules responsible for carrying out cellular __________________________________
□ Amino acids are subunit building blocks used to build polypeptide chains that form proteins
- Amino acids have an alpha carbon, a carboxyl group (COOH), an amino group (NH3), and a “R” group
- Amino acids (called residues) are linked by peptide bonds between the carboxyl group and amino group
EXAMPLE: Amino acid structure
□ Proteins function is determined by _______________________________ properties
- The 20 amino acids are arranged in a specific formation to provide the protein its function
- The properties of the side chain (R group) gives the protein unique structural and functional properties
- Can be classified as polar, charged, nonpolar or “other”
- Forms stabilizing disulfide bridges between sulfhydryl groups (SH) on the amino acid cysteine
EXAMPLE: Polypeptide chain made up of single amino acids – add extra image on structure of amino acid up!
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● Lipids are macromolecules responsible for the formation of cellular barriers; They are nonpolar = do not dissolve in H2O
□ Phospholipids are one main class of lipids responsible for the formation of bilayer membranes
- Composed of two fatty acids (long unbranched hydrocarbon chains with carboxyl group) and polar group
- They are amphipathic, which means they contain both hydrophilic and hydrophobic parts
EXAMPLE: A free fatty acid compared to a phospholipid
□ Fats are a second class of lipids responsible for energy _____________________________
- Triglycerides are composed of three fatty acids, linked by an ester bond to a glycerol molecule
- Can be saturated if they do not contain double bonds, or unsaturated if they contain chemical bonds
- 1 gram of fat stores twice the energy of 1 gram of carbohydrate
EXAMPLE: Triglyceride structure
□ Steroids are a class of lipids responsible for hormone signaling and membrane structure
- Composed of a ringed hydrocarbon skeleton
- Cholesterol is a common example found in cellular membranes that provided rigidity
EXAMPLE: Structure of cholesterol
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PRACTICE
1. Which of the following is false?
a. Polysaccharides are responsible for energy storage and cellular support
b. Nucleic acids are linked via Phosphodiester bonds
c. Amino acid sequence and structure provide proteins with unique physical attributes
d. Fatty acids are composed of branched hydrocarbon chains
2. Which of the following macromolecules does the cell use for structure and support?
a. Polysaccharides
b. Nucleic Acids
c. Lipids
d. Proteins
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3. Animal cells store excess sugar in the form of what?

a. Starch
b. Cellulose
c. Amylose
d. Glycogen
4. True or False: Polysaccharides are the macromolecules that act as a source of energy storage.
a. True
b. False
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CONCEPT: PROPERTIES OF MACROMOLECULES
Macromolecule Polymerization
● Linear polymerization forms the structures of polysaccharides, nucleic acids, and proteins (NOT lipids!)
□ Condensation reactions form the _________________________ between monomers (subunits)
- Monomer H + molecule OH group react and release water
- Repetition of condensation reactions sequentially add monomers to the macromolecule’s end
□ Hydrolysis reactions degrades long polymer chains through the addition of a water molecule
□ For proteins and amino acids, biological function depends on the specific sequence of subunits
EXAMPLE: A condensation reaction connects amino acid monomers together and results in the loss of water
Stereoisomers
● Macromolecules can be created as stereoisomers (mirror images) due to an asymmetric carbon atom (chiral center)
□ Stereoisomers are two molecules with the same chemical formula, but with different physical structures
□ Come in __________________ main forms: D- and L- forms
- Amino acids, monosaccharides, nucleic acids and steroid lipids have stereoisomer forms
- Certain biological functions only use one form (Proteins are only made up of L-amino acids)
EXAMPLE: Two amino acids stereoisomers displayed on hands to show the D- (right) and L- (left) forms
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Role of Noncovalent Bonds

● Noncovalent bonds are crucial for macromolecule formation and function
□ Although weak individually, the strength of noncovalent bonds is __________________ (more bonds = stronger)
□ Macromolecule conformation depends on placement and formation of noncovalent bonds
- Allows for a close and strong fit between two interacting molecules (Ex: multi-protein complexes)
- Macromolecule functional groups are groups of atoms that act as a unit to provide unique properties
EXAMPLE: Two potential noncovalent bonds between lysine and glutamic acid
PRACTICE:
1. Which of the following is not a property of macromolecules?
a. They are formed through linear polymerization of individual subunits
b. They have the ability to form stereoisomers
c. Noncovalent bonds allow for the formation of complex functions
d. Covalent interactions allow for stable conformations of macromolecules
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2. Which of the following reactions connects individual monomers together?

a. Hydrolysis Reactions
b. Condensation Reactions
c. Glycolyic Reactions
d. Monomeric Reactoins
3. True or False: Proteins are most often found in the D form.

a. True
b. False
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CONCEPT: PROTEIN BASICS
Protein Structures
● Proteins are made by __________________________________ amino acids

□ A polypeptide chain is formed by peptide bonds between amino acids
- A multimeric protein is made up of multiple polypeptide chains, each called a subunit
- A monomeric protein is made up of a single polypeptide.
□ The polypeptide backbone is formed with a repeating sequence of Nitrogen and Carbon atoms (-N-C-C-)
- The N-terminus contains an amino group (NH3) at it’s end
- The C-terminus contains a carboxyl group (COOH) at its end
EXAMPLE: A three amino acid polypeptide chain with N and C termini
Amino Acids
● Each amino acid in a polypeptide chain has unique properties

□ All amino acids have the same carboxyl group, an amino group, and hydrogen
□ The R group is a side chain that differs between amino acids and gives them ___________________ properties
- The polar, charged group can form ionic bonds with other charged molecules in the cell
- The polar, uncharged group can form hydrogen bonds with other molecules including water
- The nonpolar group cannot interact with water
- The other group consists of three amino acids, each with unique properties that do not fit into other groups
□ Amino acids exist as stereoisomers because the four groups are asymmetrically arranged around the α-carbon
- Two forms D- and L-; BUT the L forms is used in proteins

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EXAMPLE: A model of the structure of each amino acid
EXAMPLE: The 20 amino acid structures, classified by group
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Self-Assembly and Protein Folding
● Proteins form into _______________________ shapes

□ Most proteins are capable of self-assembly, meaning they can fold into their shape without assistance
- Information required to specific the folding is inherent in the amino acid side chains (R group)
- If the protein is denatured (unfolded) in one condition it will renature (reform) in proper conditions
□ The peptide bonds in the polypeptide backbone ___________________________ movement
- First limit on protein folding
EXAMPLE: Example of denatured and renatured forms of a protein
□ The protein’s conformation (folded shape) is determined through the properties of the amino acid R group
- This forms with conformation with the ________________________________ Gibbs free energy
- The native state of a protein specifies a small number of conformations the protein will actually form
- Out of 1000s of possibilities
□ The protein’s conformation (folded shape) is formed through noncovalent interactions
- Hydrogen bonds, Ionic bonds, Van der Waals interactions, and hydrophobic interactions
□ Disulfide bonds are stabilizing covalent bonds formed between sulfur atoms on two cysteine amino acids
EXAMPLE: Protein conformation is dictated by amino acid side chains
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● Chaperone proteins are proteins that can ________________________________ in protein folding

□ One group is the molecular chaperones that assist in stabilizing unfolded or partially folded proteins
- Bind to short segments of the protein substrate
- Prevent aggregation of unfolded, or misfolded proteins
- Hsp70 is an example
□ The second group is the chaperonins, which form small folding chambers to sequester unfolded proteins
- The sequestering allows the protein to refold without influence from molecules or water in cytosol
- Contain a cylindrical folding core, and regulated by protein “lids” that allow proteins in and out
- Hsp60 is an example
□ Chaperones _______________________________ proteins from energy provided by ATP hydrolysis
□ Misfolded proteins results in diseases like Parkinson’s, and Alzheimer’s
EXAMPLE: Structure of a chaperonin
Four Protein Models
● There are four ways to present a protein’s structure

□ The backbone model presents the overall organization of the polypeptide chain
□ The ribbon model shows the polypeptide backbone folding
□ The wire model shows the polypeptide backbone and the amino acid side chains
□ The space-filling model shows a contour map of the protein’s surface
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EXAMPLE: Four models of protein folding
Backbone model
Ribbon model
Wire model
Space Filling model
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PRACTICE
1. Which of the following is false about the R group of amino acids?
a. They give polypeptide chains unique properties
b. They assist in forming complex protein structures
c. They control the stereoisomer form of the amino acid
d. They can be nonpolar
2. A protein C-terminus is named that way because it contains what molecule?

a. An extra carbon
b. A COOH group
c. A CH3 group
d. A Chloride
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3. A protein’s conformation is formed through all but which of the following?

a. Hydrophobic Interactions
b. Disulfide bonds
c. Covalent bonds between carbons
d. Noncovalent bonds between R groups
4. Which of the following protein models would you use if you wanted to gain an idea of what the surface of a protein
looked like?
a. Backbone
b. Ribbon
c. Wire
d. Space-Filing
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CONCEPT: PROTEIN FOLDING
Primary Structure
● Primary structure is the first of four protein folding levels

□ Primary structure is the ___________________________ sequence of amino acids in a polypeptide chain
□ The sequence of amino acids, and their attached R groups provides information for folding the 3D conformation
□ Covalent peptide bonds between amino acids hold together the primary structure
EXAMPLE: Primary structure of a protein
Secondary Structure
● The secondary structure refers to _____________________________ structures formed by the polypeptide backbone.
□ The alpha helix is one secondary folding pattern
- Hydrogen bonds made between every fourth amino acid (carboxyl group bound to amino group)
- Forms a rigid cylinder that can be right handed or left handed
- Is abundant in skin protein
□ A beta sheet is another main secondary folding pattern
- Hydrogen bonds made between segments of the polypeptide chain that are arranged side by side
- Can be parallel (two chains in the same direction) or antiparallel (two chains in opposite directions)
- Is abundant in silk proteins

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□ Disulfide bonds between the side chains of cysteine can link proteins together and increase stability
EXAMPLE: Secondary structure of a protein
Tertiary Structure
● The tertiary structure refers to ____ conformations formed by a single polypeptide chain. Can be functional or structural
□ Structural motifs are combinations of two or more secondary structures that form a 3D structure
- A coiled coil is 2-3 helices that wrap around each other to form a very stable structure
- The helix-turn-helix and helix-loop-helix are two common structural motifs named by their helical structure
- Each structural motif usually has a specific function
□ Protein domains are segments of the polypeptide chain (40-350 aa) that fold into independent stable structures
- Each domain usually has a specific _________________________________
- Certain domains are found in multiple proteins (SH2 domains is found in 120 polypeptide chains)
- Domain shuffling is an evolutionary process that linked domains in new combinations
- Two-thirds of proteins contain 2+ domains
□ Tertiary structure forms two main protein types: Fibrous proteins and Globular proteins
- Fibrous proteins are proteins with an elongated shape
- Globular proteins are proteins with a compact shape
EXAMPLE: Tertiary structure of a protein

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Quaternary Structure
● The quaternary structure refers to a protein complex with _______________________________ one polypeptide chain
□ Only found in multimeric proteins which are composed of 2+ polypeptide chains
□ A subunit is a single polypeptide chain which is a part of a larger protein complex
- Each subunit can be identical or non-identical to other subunits
- A homomeric proteins: composed of identical subunits
- A heteromeric proteins: composed of non-identical subunits
□ Quaternary structure is stabilized by the same non-covalent interactions and disulfide bonds as tertiary structure
- Hydrogen bonds, van der Waals forces, hydrophobic interactions, ionic bonds
EXAMPLE: Quaternary structure of a protein
Unstructured Regions of a Protein
● Unstructured regions (disordered regions) exist between _______________________ protein structures or domains
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□ Provide flexibility to protein structure and folding
- Wrap around target proteins with high specificity but low affinity
- Can help scaffold proteins together
□ Nearly one-third of eukaryotic proteins have unstructured regions in at least one polypeptide chain
- Some can be found as the ___________________ polypeptide chain – usually form aggregates in cytosol
□ Disulfide bonds between the side chains of cysteine can link proteins together and increase stability
EXAMPLE: Unstructured regions of a protein (grey) surround structured regions (red/blue)
PRACTICE
1. Match the following protein structures with their appropriate definitions
i. Primary Structure _____________
ii. Secondary Structure _____________
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iii. Tertiary Structure _____________

iv. Quaternary Structure _____________
A. 3D conformation of a single polypeptide chain

B. Linear sequence of amino acids
C. Folding of multiple polypeptide chains together
D. Local structures of a single polypeptide chain
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CONCEPT: STUDYING PROTEINS
● Scientists use a variety of _________________________________ to study protein structure and function

□ SDS Polyacrylamide gel-electrophoresis (SDS-PAGE) is used to detect proteins
- Protein solutions are run through a polyacrylamide matrix (contains adjustable pores for migration)
- Proteins unfold when attached to negatively charged SDS, and therefore migrate in response to + charge
- The gel is then transferred onto nitrocellulose paper via a second electric field
- The membrane is then immunoblotted with antibodies to identify if proteins are present
□ 2D Gel electrophoresis can separate up to 2000 proteins on one membrane
- Proteins are separated by intrinsic charges and pH
EXAMPLE: SDS PAGE
A B
100
50
25
□ Mass spectroscopy is used to identify unknown proteins
- Samples __________________________ peptides via a mass to charge ratio
- Provides sequences of proteins from unknown protein solutions
□ Nuclear magnetic resonance spectroscopy (NMR) is used to analyze structures of proteins in solution
□ Yeast-two hybrid system is able to examine if two proteins interact inside a living organisms
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- Two proteins of interest (called “bait” or “prey”) are fused to transcription factors
- If bait and prey proteins interact, then the transcription factors interact
- The interaction is created so that when the bait and prey interact it activates transcription of a gene
EXAMPLE: Yeast two hybrid system
Bait Prey
Transcription
Promoter Reporter Gene
PRACTICE:
1. Which method would be best to use if you wanted to identify unknown proteins?
a. SDS-PAGE
b. Mass Spec
c. NMR
d. Yeast two-hybrid test
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2. Which method would be best to use if you wanted to analyze the structure of a protein?
a. SDS-PAGE
b. Mass Spec
c. NMR
d. Yeast two-hybrid test
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CONCEPT: TRACKING PROTEINS IN CELLS
● It is important for researchers to be able to find and monitor a molecule’s ________________________ in a cell
□ In situ hybridization can identify where a particular RNA or DNA is in the cell
- Incubates probes labeled with fluorescence or radioactivity with fixed cells
□ Reporter genes can be fused to proteins to identify a protein’s location or movement in a cell
- Green fluorescent protein (GFP) is a protein that has a green fluorescence
- When fused to a recombinant protein, GFP will mark the protein of interest with green fluorescence
□ When available, antibodies can also be used to identify a protein’s location in a cell
EXAMPLE:
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CELL BIOLOGY - COOPER 4E

CH. 2-THE COMPOSITIONS OF CELLS

CONCEPT: SMALL MOLECULES

● The properties of water are crucial for cell activity

- Water makes up >70% of the cell’s weight

- In water hydrophilic molecules dissolve, hydrophobic molecules do not dissolve

- Cohesion allows water to act as a temperature stabilizing molecule

EXAMPLE: Water molecule demonstrating polarity

● The properties of carbon are also crucial for cell activity

- Most likely to bond with Oxygen, Hydrogen, Nitrogen, and Sulfur

EXAMPLE: Carbon stereoisomers

1. Which of the following is not a property of water?

2. Which type of molecule dissolves in water?

3. A carbon atom can bind how many independent molecules at once?

CONCEPT: FOUR CLASSES OF MACROMOLECULES

□ Monosaccharides are the building blocks that make up ________________________ polysaccharides

- Can form into linear or ring structures – (CH2O)n

□ Aldose and Ketose are the two _______________________ of polysaccharides

EXAMPLE: Ketose (C=O in middle) vs. Aldose structure (C=O on end)

- In animal cells, glycogen stores surplus chemical energy

□ Sugars are named by the ______________________________ of subunits they contain

- Mono- = 1 subunit; Di- = 2 subunits; Oligo- = up to 10 subunits, Poly- = 11+ subunits

EXAMPLE: Amylose is a linear polysaccharide made up of α(1→4) bonds

□ Phosphodiester bonds are responsible for ____________________________ nucleic acids together

- Linear sequence of nucleic acids is important because it encodes genetic information

□ Nucleotides can also store energy

EXAMPLE: Complementary nucleotides bound in a DNA molecule

● Proteins are macromolecules responsible for carrying out cellular __________________________________

EXAMPLE: Amino acid structure

□ Proteins function is determined by _______________________________ properties

- Can be classified as polar, charged, nonpolar or “other”

EXAMPLE: A free fatty acid compared to a phospholipid

□ Fats are a second class of lipids responsible for energy _____________________________

- 1 gram of fat stores twice the energy of 1 gram of carbohydrate

EXAMPLE: Triglyceride structure

- Composed of a ringed hydrocarbon skeleton

- Cholesterol is a common example found in cellular membranes that provided rigidity

EXAMPLE: Structure of cholesterol

3. Animal cells store excess sugar in the form of what?

CONCEPT: PROPERTIES OF MACROMOLECULES

- Monomer H + molecule OH group react and release water

- Repetition of condensation reactions sequentially add monomers to the macromolecule’s end

□ Come in __________________ main forms: D- and L- forms

Role of Noncovalent Bonds

□ Macromolecule conformation depends on placement and formation of noncovalent bonds

2. Which of the following reactions connects individual monomers together?

3. True or False: Proteins are most often found in the D form.

CONCEPT: PROTEIN BASICS

● Proteins are made by __________________________________ amino acids

- A multimeric protein is made up of multiple polypeptide chains, each called a subunit

- A monomeric protein is made up of a single polypeptide.

- The N-terminus contains an amino group (NH3) at it’s end

- The C-terminus contains a carboxyl group (COOH) at its end

EXAMPLE: A three amino acid polypeptide chain with N and C termini

● Each amino acid in a polypeptide chain has unique properties

- The nonpolar group cannot interact with water

- Two forms D- and L-; BUT the L forms is used in proteins

EXAMPLE: A model of the structure of each amino acid

EXAMPLE: The 20 amino acid structures, classified by group

Self-Assembly and Protein Folding

● Proteins form into _______________________ shapes

□ The peptide bonds in the polypeptide backbone ___________________________ movement

- First limit on protein folding